In brain anatomy lab (dissection training) in medical schools, it is essential to learn localization and shape of neural structures, such as fiber bundles and neuronal nuclei. Students learn these from not only text books, but also from observations of real human brain dissected from cadavers. Although some textbooks recommend to carry out these observations just in the cutting surface of the brainstem, discrimination of white and gray matter is difficult, especially when the size of the neural structures is between macroscopic and microscopic levels. A staining method invented by Mulligan stains cerebral cortex of the human brain for macroscopic observations, and clearly distinguishes it from the white matter. However, reproducible results of staining were not obtained by the original protocol, when brain stem regions were examined. Here, we propose improvements in Mulligan staining method to be applicable to cross sections of the brain stem regions. Because we aim to use the method in training of macroscopic brain anatomy in medical schools, we made efforts to reduce steps and time for this staining. The images obtained by our modified Mulligan staining and Klüver-Barrera staining were compared in the midbrain and pons, and found that our method can identify some neural structures, which were difficult to identify without staining. Because our method use only three solutions and comprised by 6 steps, this method is useful for the training of macroscopic brain anatomy for undergraduate students.